New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1973115 =	5 (0.250)	15 (0.760)	15/270	NT	75.0%	intergenic (‑661/‑119)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 3577555	NA (NA)					intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E

TAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTCGCTGT  >  CP009273/1972972‑1973262                                                                                                                                                |                                                                                                                                                    tAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCt                                                                                                                                                >  1:209545/1‑149 (MQ=255)         aacctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACtaat                                                                                                                                        >  1:278404‑M1/136‑149 (MQ=255)          acctgaatctgaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTActaatc                                                                                                                                       <  1:356608‑M1/15‑2 (MQ=255)              gaaacctaggcagcacctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaacaagttggagtcattaccTTATCTTTACTAATAATCa                                                                                                                                   >  1:81510‑M1/131‑149 (MQ=255)                            acctggcacggctgggacggaagtcgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTAcc                                                                                                                     <  1:126124‑M1/33‑1 (MQ=255)                                 gttaatgAAATGGTTTACATATATTAACCACTTGTTTAATGCGGAGAATAAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGCGATAGATTGATTATCATTAggggatgctgccaacttaccgat                                                                                                                      <  2:69465‑M2/143‑24 (MQ=255)                                  ttaatgAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATGTTTAggtgatgctgccaacttactgatttagtgt                                                                                                               <  1:31581‑M2/149‑31 (MQ=255)                                  ttaatgAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAAAAtttcac                                                                                                                     >  2:119470/1‑140 (MQ=255)                                       gAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGa                                                                                                          >  1:263265/1‑149 (MQ=255)                                       ctgggacggaagtcgctgtcggtctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGttt                                                                                                                >  2:94646‑M1/106‑143 (MQ=255)                                                tACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgttttt                                                                                                 >  1:258472‑M2/1‑105 (MQ=255)                                                    cgctgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggtattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGcgt                                                                                             >  1:56606‑M1/93‑149 (MQ=255)                                                        gtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCCGACTAATATTTACCTGTTTGACCGAGTTCGGAATGc                                                                                               <  2:94421‑M1/55‑1 (MQ=255)                                                         gcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGttt                                                                                        >  1:59775‑M1/88‑149 (MQ=255)                                                          aaCCACTTGTTTAATGCGTAGAATCAGTACACTATTTTCTTATCATTACAGTTGAAATTATATGATCACCGCGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgagg                                                                                             >  2:147914‑M2/1‑95 (MQ=255)                                                          aaCCACTTGTTGAATGCGGAGAATCAGTACCCGACATTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTTATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGcgt                                                                                             <  2:148731/143‑1 (MQ=255)                                                           ggtctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCCGTTTCACCGAGTTGGGATTGCGTCGTTtct                                                                                      >  1:190736‑M1/86‑149 (MQ=255)                                                                  aaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTtctc                                                                                     <  2:147753‑M1/65‑1 (MQ=255)                                                                              ctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGtag                                                                         <  2:288998‑M1/77‑2 (MQ=255)                                                                                  cAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgttttttttgtttttctgtggcttctgtttctat                                                                     <  2:270017‑M2/143‑73 (MQ=255)                                                                                  cAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctg                                                               <  1:353772‑M2/149‑79 (MQ=255)                                                                                                 tggcgtatctgaacattaaacactttctatgtgttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTGGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGaa                                                      >  2:272542‑M1/48‑143 (MQ=255)                                                                                                     aaTTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCGCCTGAAGTTCACAGaa                                            >  1:13067/1‑149 (MQ=255)                                                                                                            tttGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactg                                           <  2:322227‑M2/143‑99 (MQ=255)                                                                                                            atcataaaacactatctataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGaa                                     >  1:255547‑M1/37‑149 (MQ=255)                                                                                                             tggaaATTATATGATCACCGGGAGTCATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtctgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggt                                    >  1:77388‑M2/3‑44 (MQ=255)                                                                                                               gAAATTATATGATCACCGGGGGTTATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtgg                                  >  1:30044‑M2/1‑42 (MQ=255)                                                                                                               gAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtgg                                  <  1:21756‑M2/149‑108 (MQ=255)                                                                                                                   aacactatcaatatgttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGAAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAAc                                    <  2:199289‑M1/114‑1 (MQ=255)                                                                                                                        tatcaataagttggagtcattaccTTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGc                         <  1:263632‑M1/125‑1 (MQ=255)                                                                                                                          aTCACCGGGAGTGATTGATTAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggc                       >  1:313201‑M2/1‑31 (MQ=255)                                                                                                                                     ggattgattaAGTATCTTTAtgtggtgccctcaacttactgatttagtgtatgatggtgttctcgaggttctccagtggcttctgttgctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaag                  >  2:10575‑M2/2‑20 (MQ=255)                                                                                                                                        ttgattAATTATCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcac               <  2:59780‑M2/143‑127 (MQ=255)                                                                                                                                           attaattaTCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATACGGAACAGCTTATGAGCTATAGCCATATTc            >  2:23053/1‑143 (MQ=255)                                                                                                                                               attaTCTTTAggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggttctccagtggcttctgtttctatcagctgtccctcctgttcagctactgacggggtggtgcgtaacggcaaaagcactgccggacatcag  >  1:20554‑M2/1‑10 (MQ=255)                                                                                                                                                ttaTCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTc       <  2:111869/143‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    TAAATACAAAGAAAGGCAACAATCAACTTAATGTTAATGAAATGTTTTACATATATTAACCACTTGTTTAATGCGGAGAATCAGTACACTATTTTCTTATAATTACATTTGAAATTATATGATCACCGGGAGTGATTGATTAATTATCTTTACTAATAATCAGACTAATATTTACCTGTTTGACCGAGTTGGGATTGCGTCGTTTCTCCATTAGGAGTAAAGCTTTAATGTCACCTGAAGTTCACAGAATAAGGAACAGGTTATGAGCTATAGCAATATTCTTGTCGCTGT  >  CP009273/1972972‑1973262

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.